tbuckley/cabot-search huggingface dataset:
Abstract 125: Archival single cell sequencing reveals persistent subclones over years to decades of DCIS progression
Authors: Kaile Wang, Tapsi Kumar, Junke wang, Darlan Minussi, Emi Sei, Jianzhuo li, Tuan Tran, Aatish Thennavan, Min Hu, Anna Casasent, Zhenna Xiao, Shanshan Bai, Yuehui Zhao, Amado Zurita, Ana Aparicio, Brian Chapin, Jie ye, Jianjun Zhang, Don Gibbons, Andrew Futreal, Lorraine King, Jeffrey Marks, E. Shelley Hwang, Vandna Shah, Ellinor Sawyer, Petra Kristel, Jelle Wesseling, Esther H. Lips, Nicholas Navin
Journal: Cancer Research (2023)

Abstract Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer (IBC), yet the genomic progression to recurrent disease remains poorly understood. A main contributor to this gap in knowledge arises from technical challenges with genomic profiling of formalin-fixed paraffin-embedded (FFPE) materials. To address this challenge, we developed Arc-well, the first high-throughput method that can perform single cell DNA sequencing of thousands of cells from FFPE materials and frozen tissues. Using Arc-well, we profiled genomic copy number in 27,851 single cells from 26 archival FFPE tissues that were stored for 3-31 years. Analysis of genomic evolution in 10 patients with matched DCIS and recurrent cancers (DCIS or IBC) separated by 2-16 years showed that many primary DCIS lesions had already undergone whole-genome-doubling and had extensive clonal diversity, similar to the paired recurrence. The data from most patients (8/10) suggest an evolutionary bottleneck model of progression, in which a single subclone persisted during the progression to the recurrent disease, revealing copy number aberrations associated with invasion and recurrence. Citation Format: Kaile Wang, Tapsi Kumar, Junke wang, Darlan Minussi, Emi Sei, Jianzhuo li, Tuan Tran, Aatish Thennavan, Min Hu, Anna Casasent, Zhenna Xiao, Shanshan Bai, Yuehui Zhao, Amado Zurita, Ana Aparicio, Brian Chapin, Jie ye, Jianjun Zhang, Don Gibbons, Andrew Futreal, Lorraine King, Jeffrey Marks, E. Shelley Hwang, Vandna Shah, Ellinor Sawyer, Petra Kristel, Jelle Wesseling, Esther H. Lips, Nicholas Navin. Archival single cell sequencing reveals persistent subclones over years to decades of DCIS progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 125.
Abstract 1749: The synergic effect of cisplatin and a chemokine receptor antagonist sensitizes drug resistant gastric cancer cells and inhibits tumoroid formation
Authors: Bárbara Mora-Lagos, María Elena Reyes, Lorena Lobos-Gonzalez, Matías del Campo, Carmen Gloria Ili, Kurt Buchegger, Yuselin Mora, Louise Zanella, Ismael Riquelme, Priscilla Brebi
Journal: Cancer Research (2023)

Abstract Introduction: Gastric cancer (GC) is an important cause of death worldwide. Cisplatin (CDDP) is the most used drug in the chemotherapy of advanced GC. However, CDDP resistance reduces GC survival. The CCR5/CCL5 axis has been associated with GC development, but its role in CDDP resistance in GC has not been elucidated. The aim of this study was to determine the effects of CCR5/CCL5 axis blockade by a chemokine receptor antagonist (CRA), alone and in combination with CDDP, on in vitro and 3D tumorid models from AGS R-CDDP cells. Methodology: AGS R-CDDP cells (CDDP-resistant human gastric adenocarcinoma cells) were previously established using a stepwise drug dosing protocol and characterized. CCL5 was selected through transcriptomic analysis and its expression level was validated by qRT-PCR. Cytotoxicity assays were determined by using MTT. Apoptosis and cell cycle assays were evaluated by flow cytometry. Tumoroid formation was performed from AGS R-CDDP cells in low adhesion plates (NunclonTMSpheraTM). After 10 days in culture, tumoroid &amp;gt;150 µm in diameter were scored and pharmacological stimuli were added on days 14, 17 and 20. CRA was used alone and in combination with CDDP in all assays. Results: CRA/CDDP combination triggered a re-sensitized phenotype in AGS R-CDDP cells, decreasing cell viability but not increasing apoptosis compared to independent treatments. AGS R-CDDP cells treated with CRA/CDDP were mainly arrested in S phase. CCL5 showed a decrease in mRNA levels after the CRA/CDDP combination compared to separate treatments. AGS R-CDDP cells showed a higher potential in the ability to form tumoroids compared to AGS WT cells. Finally, CRA/CDDP combination inhibited tumoroid formation compared to independent treatments. Discussion and Conclusion: CCL5 showed a decrease in mRNA levels after the CRA/CDDP combination, possibly correlating with allosteric inhibition of the CCR5 receptor. CRA/CDDP combination has a synergic effect that sensitizes AGS R-CDDP cells and inhibits tumoroid formation. This combination could be used as a potential coadjuvant in GC therapy allowing to reduce the doses of CDDP and therefore to reduce side effects. Citation Format: Bárbara Mora-Lagos, María Elena Reyes, Lorena Lobos-Gonzalez, Matías del Campo, Carmen Gloria Ili, Kurt Buchegger, Yuselin Mora, Louise Zanella, Ismael Riquelme, Priscilla Brebi. The synergic effect of cisplatin and a chemokine receptor antagonist sensitizes drug resistant gastric cancer cells and inhibits tumoroid formation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1749.
Abstract 5579: Single cell characterization of circulating plasma cells and BCMA levels in patients with multiple myeloma
Authors: Sonia Maryam Setayesh, Stephanie Shishido, Libere Ndacayisaba, Amin Naghdloo, Jeremy Mason, Dean Tessone, Carli Kaleta, Robert Z. Orlowski, Elisabet E. Manasanch, James Hicks, Peter Kuhn
Journal: Cancer Research (2023)

Abstract Multiple myeloma (MM), a disease caused by the clonal proliferation of plasma cells (PCs), is the second leading hematologic malignancy in the world, with a global incidence rate increase of 126% and mortality rate increasing by 94% in the past decade. Recently, B cell maturation antigen (BCMA) has emerged as a promising biomarker and therapeutic target for MM due to its selective high expression on malignant PCs, improving the treatment landscape. However, the current diagnostic workup relies on bone marrow aspirates (BMA) which are highly invasive and do not allow for the detection of BCMA levels on circulating PCs, severely limiting the options for repeatable assessments and treatment-monitoring. In our study, we report the utility of a blood-based liquid biopsy, using enrichment-free high definition single cell assay (HDSCA) for the detection, quantification, and morphological characterization of circulating PCs and other BCMA+ cells. We applied a previously validated 4-color immunofluorescence assay using DAPI, CD138, BCMA, and CD45 to examine matched peripheral blood and BMAs from 68 patients across the MM disease spectrum (11 monoclonal gammopathy of undetermined significance [MGUS], 21 smoldering MM [SMM], 18 newly diagnosed MM, and 18 relapsed refractory MM [RRMM]) and peripheral blood from 23 normal donors as controls. Our analysis revealed diverse subtypes of circulating CD138(+/-), BCMA(+/-), and CD45(+/-) cells across the patients, representing both normal and abnormal PCs. We detected significantly higher circulating CD138+ BCMA(+/-) cells in MM precursor conditions (MGUS, SMM), compared to the normal donors. Additionally, we were able to detect BCMA+ oncosomes (identified by the lack of a nuclear structure) in the circulation of patients from both precursor and overt disease conditions. Our findings establish the utility of HDSCA blood-based liquid biopsy for early disease detection and anti-BCMA therapy response monitoring in MM and other B-cell malignancies expressing BCMA. Citation Format: Sonia Maryam Setayesh, Stephanie Shishido, Libere Ndacayisaba, Amin Naghdloo, Jeremy Mason, Dean Tessone, Carli Kaleta, Robert Z. Orlowski, Elisabet E. Manasanch, James Hicks, Peter Kuhn. Single cell characterization of circulating plasma cells and BCMA levels in patients with multiple myeloma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5579.
Abstract 5174: PEGylated liposomal doxorubicin improves oral cancer response to radio-immunotherapy
Authors: Laxman Devkota, Rohan Bhavane, Andrew Badachhape, Ratna Veeramachaneni, Renuka Menon, Prajwal Bhandari, Sofia Cortes, Fabio Henrique Brasil Da Costa, Ketan Ghaghada, Simon Young, Andrew G. Sikora, Ananth V. Annapragada
Journal: Cancer Research (2023)

Abstract Introduction: The immunosuppressive tumor microenvironment (TME) in oral cancer inhibits response to conventional treatment (surgery +/- chemoradiotherapy) and check-point inhibitor (αPD1) immunotherapy. The chemotherapeutic agent doxorubicin and its PEGylated liposomal nanoparticle formulation (PLD) have been shown to target myeloid derived suppressor cells (MDSCs) in the TME. In this preclinical work, we investigated whether PLD improves response to radio-immunotherapy in a highly aggressive and immunologically ‘cold’ oral cancer model. Experimental Procedure: Studies were performed in the MOC2 syngeneic mouse model of oral cancer. Mice were randomized to one of seven treatment groups: αPD1, Radiation (XRT), αPD1+XRT, PLD, PLD+αPD1, PLD+XRT, PLD+αPD1+XRT. High-resolution nanoparticle contrast-enhanced computed tomography (nCECT) imaging was performed, and whole-body T2-weighted magnetic resonance imaging (MRI) used to monitor primary tumor response and development of metastases. Response evaluation criteria in solid tumors (RECIST) were used to evaluate treatment outcomes. Results: Tumors in all non-PLD groups were treatment resistant and grew progressively, consistent with the immunologically ‘cold’ MOC2 model. In contrast, all PLD groups showed tumor regression with 25-38% complete responders (CR) and 12-88% partial responders (PR) while all animals in non-PLD groups showed progressive disease (PD). MR imaging identified a high incidence of regional and distant metastases in the non-PLD groups while the PLD groups showed decreased regional and no distant metastases (Table 1). Presence of metastases was confirmed by nCECT imaging and histopathological analysis. Conclusion: PLD improved response to radio-immunotherapy in a highly aggressive immunologically ‘cold’ mouse model of oral cancer while simultaneously preventing disease progression and metastasis. Citation Format: Laxman Devkota, Rohan Bhavane, Andrew Badachhape, Ratna Veeramachaneni, Renuka Menon, Prajwal Bhandari, Sofia Cortes, Fabio Henrique Brasil Da Costa, Ketan Ghaghada, Simon Young, Andrew G. Sikora, Ananth V. Annapragada. PEGylated liposomal doxorubicin improves oral cancer response to radio-immunotherapy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5174.
Abstract 1529: Characterizing antibody internalization for rational selection of ADC linker design
Authors: Zekun Shao, Jayanth Panyam
Journal: Cancer Research (2023)

Abstract Antibody-drug conjugates (ADC), which target a highly potent cytotoxin to a specific protein overexpressed on tumor cells, are a promising class of anticancer therapeutics. In addition to the antibody characteristics, intracellular reactivity of the antibody-cytotoxin linker (which affects drug release) is a key determinant of ADC efficacy. While many different linkers have been used in approved ADCs, the intracellular trafficking profile of an antibody will likely impact the effectiveness of different linkers differently. Here, we determined the cellular internalization of two antibodies, anti-perlecan antibody (‘AM6’), and anti-EGFR antibody (cetuximab; ‘Ctx’), in MDA-MB-231-LM2 cells (a lung-metastatic TNBC cell line). Using live-cell confocal microscopy, we investigated the effect of endocytosis inhibitors on intracellular trafficking of AM6 and Ctx. While AM6 was internalized quicker compared to Ctx, the internalization of both antibodies was reduced significantly by 5-(N-Ethyl-N-isopropyl)-amiloride, a macropinocytosis inhibitor and, to a lesser extent, by chlorpromazine, an inhibitor of clathrin-mediated-endocytosis. The results suggest both AM6 and Ctx were internalized by both macropinocytosis and clathrin-mediated endocytosis. We then investigated whether acidic pH in the lysosomes and the reductive environment in the endosomal vesicles would facilitate drug release from ADC. We conjugated thiol-reactive doxorubicin to reduced interchain disulfides of Ctx via either the acid and glutathione (GSH)-labile pyridinyldithio-hydrazide linker or the non-cleavable C6-maleimide linker. Intracellular doxorubicin release for the two ADCs was evaluated by live-cell confocal microscopy. Doxorubicin was successfully conjugated to Ctx, with a DAR of 4.8 and 8.6 for the cleavable and non-cleavable linkers, respectively. Conjugation of doxorubicin to the antibody was confirmed by fluorescent gel imaging after SDS-PAGE and by using hydrophobic interaction chromatography. Confocal microscopic studies showed that the ADC with cleavable linker resulted in greater doxorubicin accumulation in the nucleus compared to the ADC with non-cleavable linker, which was predominantly sequestered in the lysosomes. These results suggest that the cleavable linker results in better drug release compared to the non-cleavable linker for the Ctx-doxorubicin ADC. Studies examining the effect of linker chemistry on drug release from the anti-perlecan ADC and on the anticancer efficacy of the two ADCs are ongoing. Citation Format: Zekun Shao, Jayanth Panyam. Characterizing antibody internalization for rational selection of ADC linker design [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1529.
Abstract 6571: Mammonc-DB: A web based user-friendly tool for comprehensive multi-omics data analysis in breast cancer
Authors: Santhosh Kumar Karthikeyan, Darshan S. Chandrashekar, Upender Manne, Chad Creighton, Zhaohui S. Qin, Sidharth Kumar, Sooryanaraya Varambally
Journal: Cancer Research (2023)

Abstract Breast cancer (BC) accounted for 15% cancer related death among women, in the United States last year. It is a highly heterogeneous and complex diseases with multiple molecular events occurring during cancer initiation and progression. It is important to unravel the heterogeneity of breast cancer and the molecular events to develop diagnostic biomarkers and targeted therapies. There is need for comprehensive and user-friendly tool for the utilization of available breast cancer data including metastatic and treatment response data. We have earlier created a highly used pan-cancer proteogenomic portal called UALCAN (ualcan.path.uab.edu). Based on the current unmet need for comprehensive BC data analysis and visualization resource, we developed an integrated proteo-genomicbreast cancer data analysis portal, called Mammonc-DB (http://resource.path.uab.edu/MammOnc-ge.html). For Mammonc-DB, we collected data from public repositories like NCBI Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) for collecting and analysis of genomics and epigenetics data, and, PRIDE, and, ProteomeXchange for proteomics data. We procured and processed multi-omics studies related to normal, primary, and metastatic human breast cancer data with other clinical information available, for different clinical models. We also collected and analyzed different therapy, and treatment studies that are currently employed in treating BC patients. Mammonc-DB has user friendly interface that aid breast cancer researchers and clinicians in, a) allows users to identify potential biomarkers in breast cancer, b) accessing publicly available breast cancer multi-omics data, c) Visualizing the expression pattern of gene or protein of interest with clinical feature stratification in each dataset among others This resource serves as a one-stop resource to study gene expression (protein-coding and non-coding) analysis along with epigenetic regulation, and protein expression patterns in BC. With this platform, we tend to create global user base that will accelerate discovery of biomarkers in BC that might be involved in diagnosis, therapeutic target identification and treatments of breast cancer. Citation Format: Santhosh Kumar Karthikeyan, Darshan S. Chandrashekar, Upender Manne, Chad Creighton, Zhaohui S. Qin, Sidharth Kumar, Sooryanaraya Varambally. Mammonc-DB: A web based user-friendly tool for comprehensive multi-omics data analysis in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6571.
Abstract 5913: Semi-supervised analysis of myeloid and T cell behavior in <i>ex vivo</i> ovarian tumor slices reveals changes in cell motility after treatments
Authors: Florian Laforets, Panoraia Kotantaki, Beatrice Malacrida, Samar Elorbany, Ranjit Manchanda, Emmanuel Donnadieu, Frances Balkwill
Journal: Cancer Research (2023)

Abstract Cell motility is an important component of anti-tumor responses, allowing immune cells like myeloid and cytotoxic T cells to infiltrate tumors. Using ex vivo human and mouse high-grade serous ovarian cancer (HGSOC) tumor slices combined with time-lapse imaging, we monitored the movement of CD8+ T and myeloid cells in live tumors, in real-time. To analyze the recordings and characterize immune cell movements, we developed a semi-supervised analysis, identifying four types of cell behavior: migrating, long migrating, static and wobbling. Tumor slices were maintained 24h ex vivo, retaining viability and cell movements. We show that ex vivo treatments with LPS altered CD8+ T and myeloid cell behavior. In vivo chemotherapy reduced ex vivo cell movements in human and mouse tumors, and differentially affected CD8+ T and myeloid cells in 60577 and HGS2 murine tumors, respectively chemo-sensitive and chemo-resistant mouse models, suggesting those cell types have different roles in the response to chemotherapy. Ex vivo tumor slices can extend in vivo mouse work to human, providing a stepping stone to translate mouse cancer studies to clinical trials. Citation Format: Florian Laforets, Panoraia Kotantaki, Beatrice Malacrida, Samar Elorbany, Ranjit Manchanda, Emmanuel Donnadieu, Frances Balkwill. Semi-supervised analysis of myeloid and T cell behavior in ex vivo ovarian tumor slices reveals changes in cell motility after treatments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5913.
Abstract 2194: Performance of a 24-hour turnaround, guideline-complete NSCLC assay, optimized for sparse samples
Authors: Kerri Cabrera, Jeff Gole, Bryan Leatham, Isabel Regoli, Tiffany Martinez, Andrew Richards, Leah Herdt, Juan Enciso, Paige Berroteran, Heather Carolan, Brad Brown
Journal: Cancer Research (2023)

Abstract Non-Small Cell Lung Cancer (NSCLC) is the most common type of lung cancer with 236,740 new cases diagnosed in 2022 in the United States. In this study, we demonstrate the performance of a digital PCR (dPCR) based assay that reports 15 (NCCN) biomarkers using only 1 slide of FFPE tissue. ChromaCode’s High Definition PCR (HDPCR™) NSCLC Tumor Profiling Panel (Research Use Only) detects guideline biomarkers including variants for EGFR, BRAF, KRAS, ERBB2, ALK, ROS1, RET, MET, and NTRK1-3 with a 24 hour turnaround time and a simple PCR workflow. A total of 34 NSCLC FFPE specimens were evaluated using the HDPCR NSCLC Panel. DNA and RNA were extracted from a single 10 µm section of specimen, with a sister section previously characterized with the Oncomine Precision Assay GX. The DNA/RNA eluates (20ng DNA per well, 20ng RNA) were run with the HDPCR NSCLC Panel on the Qiagen QIAcuity dPCR instrument. Data analysis was conducted using ChromaCloud™, which includes a proprietary algorithm that can detect and quantify 6 targets (5 targets and 1 internal control) for each of the 3 wells. DNA samples discordant with the comparator assay were evaluated using the Archer DNA VariantPlex panel, while RNA discordant samples were analyzed using the Archer RNA fusion plex panel. Of the 34 specimens evaluated, 16 SNV, 13 Insertion/Deletion, and 7 fusion positive specimens were identified using NGS. On the dPCR assay, the results show a high-level of agreement, after discordant resolution, of 95.8% across the panel. The minor allele fraction (MAF), also calculated using ChromaCode Cloud, ranged from 5% to 90%. With 20 ng input (Qubit), the average copy number of amplifiable DNA ranged from 791 copies (~2.3 ng) to 6583 copies (~19.9 ng) with a mean of 2410 copies (~7.43 ng). Here we demonstrate that the HDPCR NSCLC Tumor Profiling Panel provides comparable performance to validated NGS assays with a turnaround that enables adherence to guideline-recommended treatment, and a low sample requirement that maximizes the number of patients for molecular testing. The standard protocols used by the assay and the use of a cloud based analysis pipeline enables easy deployment of this assay in any lab. Citation Format: Kerri Cabrera, Jeff Gole, Bryan Leatham, Isabel Regoli, Tiffany Martinez, Andrew Richards, Leah Herdt, Juan Enciso, Paige Berroteran, Heather Carolan, Brad Brown. Performance of a 24-hour turnaround, guideline-complete NSCLC assay, optimized for sparse samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2194.